Interpretive Summary: Brachypodium distachyon (Brachypodium) is emerging as an experimental model to study the grasses used for food, feed and fuel. The complete genomic sequence of an organism is a powerful experimental tool that enables the application of many modern molecular tools. This paper reports on the complete genome sequence of Brachypodium. The genome assembly and annotation were of extremely high quality as measured by the percentage of sequence contained in the chromosome-scale assemblies and the validation of predicted gene models by independent next generation DNA transcriptome sequencing and manual examination of a subset of the genes. In addition to providing a research tool, the Brachypodium genome was used for a comparative analysis of grass genomes. A pattern of whole chromosome insertions into the centromeric regions of other chromosomes was detected as a major factor in the evolution of grass genomes.

Technical Abstract:
Three subfamilies of grasses, the Ehrhartoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research,
supports the development of new energy and food crops.